Dear All,
I am interested in patterns of trait evolutionary rates. I have applied
rjmcmc.bm (R GEIGER package) using the full model (type= “jump-rbm”), but I
am having troubles interpreting the output.
Specifically, I was wondering if it’s possible to obtain a scaled tree, in
which branches are shorted/stretched to mirror evolutionary rates (similar
to the scaled tree from the output of Bayes Traits). I have tried building
this tree using the “median rates” vector provided by the model (see
example code below)
# read output of model using load.rjmcmc
res=load.rjmcmc(paste("jump-relaxedBM", "name_of_tree", sep="."), phy=NULL,
burnin=0.25)
plot(res, par="shifts", show.tip=TRUE, edge.width=2.5,cex=0.4) -> rj_rates
#reorder rj_rates data frame so that it's in the same order as
res$my_tree$edge
rj_rates<- rj_rates[match(res$my_tree$edge[,2], rj_rates$branch),]
# re-scale by multiplying my_tree branch lengths by "median.rates" column
in rj_rates data frame
res$my_tree$edge.length <-res$my_tree$edge.length * rj_rates$median.rates
Following this code, I seem to be getting shortening/stretching of branches
in my tree, but the magnitude of such transformations is smaller compared
to the scaled trees obtained by using other software. Therefore, I was
wondering about the accuracy of my assumption that the “median rates”
vector represents trait ERs estimated on each branch.
Thank you for your time!
Best wishes,
Angela
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
